DOCSLIB.ORG

Biochemistry 2 Spr 2015 Lecture # Glycogen Metabolism

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Biochemistry 2 Spr 2015 Lecture # Glycogen Metabolism Biochemistry 2 Spr 2015 Lecture # Glycogen Metabolism Glycogen Metabolism: This is another reciprocal pathway for the sequestration or the rapid release of glucose. The presence of glycogen granules in the liver, about 21nm in size, form the beta particle. Each β particle has approx 55,000 glucose residues. Approx 20-40 β-particle cluster to form α-rosette particles. The amount of glucose bound in glycogen as free glucose would bring the glucose conc to 0.4M in the cytosol, while the bound macromolecules conc is less than 0.01µM. The precise flux control of a pathway is possible when an enzyme functioning far from equilibrium is opposed by a separately controlled enzyme. Then, vf & vr vary independently & vr can be larger or smaller than vf, allowing control of both rate and direction. This is what occurs in glycogen metabolism due to there being two distinct enzymes, the phosphorylase & the synthase. Why does the body preferentially utilize glycogen before fat since fat is more abundant in the body? Muscle can not mobilize fat as efficiently as glycogen. Fatty acid residues cannot be metabolize anaerobically Animals can not convert fat to glucose Utilization of Glucose; Glucose is utilized in several pathways; • glycogen synthesis , • pentose phosphate pathway • Lipogenesis • Amino acid synthesis • Energy metabolism: both anaerobic & aerobic. Glycogen is a highly branched macromolecule that permits rapid hydrolysis (phosphorylitic cleavage) to rapidly release of glucose. Branch points are separated by 8 to 12 glucosyl residues. It can be hydrolysed from each branch of a glycogen particle simultaneously. In striated muscle glycogen is 1-2% of the cells dry weight while in liver its 10% dry weight, and in Trichomonas vaginalis or Giardia intestinalis it is 15%. Glycogen forms a left handed helix, 6.5 residues / turn. Glycogen breakdown depends on three enzymes; glycogen phosphorylase, debranching enzyme and phosphoglucomutase. Structure of rabbit muscle glycogen phosphorylase, diagram of a phosphorylase b subunit. It is a homodimer of 97kD, 842 amino acid residues/ subunit. Glycogen phosphorylase a has a PO4 group esterified to ser 14 in each each subunit. Phosphorylase is the rate limiting step in glycogen phosphoarlysis and is allosteric inhibitors ATP, G6P, glucose. The major allosteric activator AMP. Sensitivity of the phosphorylase to these modulators are dependent on whether the enzyme’s subunits are phosphorylated. X-Ray structure of rabbit muscle glycogen phosphorylase. A ribbon diagram of the glycogen phosphorylase a dimer. The dimer has a two fold axis of symmetry. In the top peptide, the N- terminal is in blue and the C- terminal in green. Glycogen is bound to the glycogen storage site, with a PO4 in the catalytic site, and AMP in the allosteric site. 30Å crevice on the surface of each monomer has the same radius as the glycogen molecule. This crevice accommodates 4-5 glucose residues, connecting the binding site to the catalytic site. It is to narrow for branched oligosacch. What problem do you then see in the rapid hydrolysis of glycogen? PLP is covalently bound and functions in this reaction differently than in amino acid metabolism. The phosphoryl group will aid in the acid-base catalysis. An interpretive “low-resolution” drawing showing the enzyme’s various ligand-binding sites. The glycogen storage site, which binds glycogen to the active site, increases the catalytic efficiency by of the phosphorylase by permitting it to phosphorylize many glucosyl residues on the same branch of a glycogen particle without having to dissociate and re- associate between catalytic cycles. The reaction mechanism of glycogen phosphorylase. This reaction results in the cleavage of the C1-OH bond from the non- reducing terminal glucosyl residue to yield G1P. The mechanism is very similar to that of Lysozyme and MTA phosphorylase. 1. Formation of a E-P -glycogen ternary complex. i 2. Formation of an oxonium ion intermediate from the α-linked terminal glucosyl residue, acid catalysis by Pi facilitated by the proton transfer from PLP. Note half chair of oxonium ion intermediate. 3.Rxn with Pi forms G1P. But how does a cell utilize G1P? The mechanism of phosphoglucomutase. Phosphorylase converts glucosyl unit of glycogen to G1P. The rxn catalysed by phosphoglucomutase is similar to phosphoglycerate mutase, intermediate form is G1,6BP. The enzyme transfers a Pi to the 6 carbon and the E is re-PO4 by the Pi on the C-1. G1,6BP dissociation leads to phosphoglucomutase inactivation. Small amounts of G1,6P are necessary to keep enzyme fully active. Phosphoglucokinase phosphorylates G-6-P in the 1 position to form G 1,6BP. Debranching enzyme acts as 1. α(1→4) transglycosylase, transfering oligosacch to non-reducing end. 2. α(1→6) glucosidase rxn, yeilding a glucose residue. Same enzyme has two different active sites. Hydrolysis of glucose 6-phosphate by glucose 6-phosphatase of the ER. The catalytic site of glucose 6-phosphatase faces the lumen of the ER. A G6P transporter (T1) carries the substrate from the cytosol to the lumen, and the products glucose and Pi pass to the cytosol on specific transporters (T2 and T3). Glucose leaves the cell via the GLUT2 transporter in the plasma membrane. Thermodymanics of glycogen metabolism • Under physiological conditions phosphorlysis of glycogen is exergonic, -5 to -8 KJ/mol • The formation of G1P under physiological condition is unfavorable, requiring free energy input. • Consequently breakdown and synthesis must be separate pathways. • This allows reciprocal controls and independent regulation of each pathway. • Since the synthesis of glycogen from G1P is thermodynamically unfavorable it requires a supply of energy. Glycogen synthesis Reaction catalyzed by UDP–glucose pyrophosphorylase. Glycogen synthesis requires and additional exergonic step, formation of UDP-glucose. Three enzymes catalyse the formation of glycogen; UDP–glucose pyrophosphorylase, glycogen synthase & glycogen branching enzyme. kJ/mol G1P +UTP→ UDPG + PPi ≈0 H2O + PPi → 2Pi -33.5 This rxn is catalysed by the enzyme UDP-glucose pyrophphorylase. This rxn is catalysed by pyrophosphate phospholytically cleaved from the UTP, this is energetically possible due to the hydrolysis of PPi →2Pi. Reaction catalyzed by glycogen synthase. The UDPG is transferred to the C4-OH of the non-reducing end of glycogen forming an α(1→4) glycosidic bond. UDP is recycled to UTP by nucleoside diphosphate kinase. Glycogen synthase can only extend an existing glucan chain. What forms the primer? Glycogenin. It forms the heptamer needed as a primer to be extended by glycogen synthase. Branching is accomplished by a separate enzyme, amylo(1,4→1,6) transglycosylase (branching enzyme). Breaking the α(1→4) is -15.5 kJ/ mol & form the α(1→6) is -7kJ/mol. Hydrolysis of the α(1→4) drives the formation of α (1→6) glycosidic bonds and branch transfer. Like the phosphorylase, the Branching causes increased solubility of synthase is regulated by covalent glycogen & increases the rate of modification. Phosphorylation has synthesis or hydrolysis. There is a opposite effects on the glycogen conserved Asp residue found in the phosphorylase & synthase. PO branching and debranching enzymes. 4 converts active synthase a into The Asp residue may bind the oligsacch inactive b form. for transfer. Muscle glycogenin (Mr 37,000) forms dimers in solution. Humans have a second isoform in liver, glycogenin-2. The substrate, UDP-glucose (shown as a red ball-and- stick structure), is bound to a Rossmann fold near the amino terminus and is some distance from the Tyr194 residues (turquoise)—15 Å from the Tyr in the same monomer, 12 Å from the Tyr in the dimeric partner. Each UDP-glucose is bound through its phosphates to a Mn2+ ion (green) that is essential to catalysis. Mn2+ is believed to function as an electron-pair acceptor (Lewis acid) to stabilize the leaving group, UDP. The glycosidic bond in the product has the same configuration about the C-1 of glucose as the substrate UDP-glucose, suggesting that the transfer of glucose from UDP to Tyr194 occurs in two steps. The first step is probably a nucleophilic attack by Asp162 (orange), forming a temporary intermediate with inverted configuration. A second nucleophilic attack by Tyr194 then restores the starting configuration, this is accomplished by tyrosine glucosyltransferase. This forms a primer on glycogenin that can be extended by glycogen synthase. The control reciprocal pathways of glycogen synthesis and phosphoroylsis As glycogen hydrolysis is activated, glycogen synthesis is being turned off, otherwise it would be a futile cycle and glycogen synthesis would be competing for glucose molecules that are for export to muscles and other tissues. These pathways are reciprocally regulated by hormone triggered [cAMP] cascades of PKA & IP3 release of Ca+2 with DAG triggered cAMP. The actions of the PKA are reversed by protein phosphatase (PP1), which has a central role in the reciprocity of these pathways. PP1 inactivates phosphorylase kinase and glycogen phosphorylase a by dephosphorylating these enzymes. It removes PO4 from inactive glycogen synthase b to convert it to the active a form. It accelerates glycogen synthesis. The structural difference between the R & T conformations are, in the T the state the enzyme active site is buried, hence the low affinity for the substrate, in the R state the enzyme has an accessible catalytic site and high affinity phosphate binding site. AMP promotes T(inactive) →R(active) conformational shift. ATP binds to the allosteric effector site in the T conformation and it inhibits the T(inactive) →R(active) shift. Major enzymatic modification/demodification systems involved in the control of glycogen metabolism in muscle. Phosphorylase kinase (PhK) is itself covalently modified. For it to be fully active Ca+2 must be present and it must be phosphorylated. cAMP activated PKA, that phosphorylates both PhK and glycogen synthase. The δ subunit of PhK is calmodulin (CaM).
Load more

Recommended publications
  • Evolutionary Genetic Studies of Mating Type and Silencing in Saccharomyces
    Evolutionary Genetic Studies of Mating Type and Silencing in Saccharomyces by Oliver Anthony Zill A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Molecular and Cell Biology in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Jasper Rine, Chair Professor Barbara Meyer Professor Michael Levine Professor Kathleen Ryan Spring 2010 Evolutionary genetic studies of mating type and silencing in Saccharomyces © 2010 by Oliver Anthony Zill Abstract Evolutionary Genetic Studies of Mating Type and Silencing in Saccharomyces by Oliver Anthony Zill Doctor of Philosophy in Molecular and Cell Biology University of California, Berkeley Professor Jasper Rine, Chair This thesis describes studies exploring the evolution of the genetic circuits regulating yeast mating-type and silencing by Sir (Silent Information Regulator) proteins in the budding yeast Saccharomyces bayanus, a close relative of the laboratory workhorse S. cerevisiae (a.k.a., budding yeast, or brewer’s yeast). The two central subjects of these studies, mating type and silencing, are textbook examples of “well understood” mechanisms of eukaryotic gene regulation: the former serves as a model for understanding the genetic control of cell-type differentiation, the latter serves as a model for understanding physically condensed, transcriptionally repressed portions of the genome, often referred to as “heterochromatin”. The two subjects are intimately connected in the biology of the budding yeast life cycle, as explained below, and I argue that a deeper appreciation of this connection is necessary for further progress in the study of either subject. My thesis brings a critical evolutionary perspective to certain assumptions underlying current knowledge of mating-type regulation and silencing—in short, an appreciation of organismal biology that has been marginalized in the pursuit of understanding molecular mechanisms.
    [Show full text]
  • An Initiator Element Mediates Autologous Down- Regulation of the Human Type a ␥-Aminobutyric Acid Receptor ␤1 Subunit Gene
    An initiator element mediates autologous down- regulation of the human type A ␥-aminobutyric acid receptor ␤1 subunit gene Shelley J. Russek, Sabita Bandyopadhyay, and David H. Farb* Laboratory of Molecular Neurobiology, Department of Pharmacology, Boston University School of Medicine, 80 East Concord Street, Boston, MA 02118 Edited by Erminio Costa, University of Illinois, Chicago, IL, and approved May 15, 2000 (received for review November 19, 1999) The regulated expression of type A ␥-aminobutyric acid receptor The ␤1 subunit gene is located in the ␤1-␣4-␣2-␥1 gene cluster (GABAAR) subunit genes is postulated to play a role in neuronal on chromosome 4 (12) and is most highly expressed in the adult maturation, synaptogenesis, and predisposition to neurological rat hippocampus. Seizure activity decreases hippocampal ␤1 disease. Increases in GABA levels and changes in GABAAR subunit mRNA levels by about 50% while increasing ␤3 levels (11). gene expression, including decreased ␤1 mRNA levels, have been Because the subtype of ␤ subunit influences the sensitivity of the observed in animal models of epilepsy. Persistent exposure to GABAAR to GABA and to allosteric modulators such as GABA down-regulates GABAAR number in primary cultures of etomidate, loreclezole, barbiturates, and mefenamic acid (13– neocortical neurons, but the regulatory mechanisms remain un- 17), a change in ␤ subunit composition may alter receptor known. Here, we report the identification of a TATA-less minimal function and pharmacology in vivo. Modulation of receptor ␤ promoter of 296 bp for the human GABAAR ␤1 subunit gene that function by phosphorylation is also influenced by subunit is neuron specific and autologously down-regulated by GABA.
    [Show full text]
  • The Hexokinase System of the Erythrocyte
    THE HEXOKINASE SYSTEM OF THE ERYTHROCYTE by Charles Prévost A thesis submitted to the Faculty of Graduate Studies and Research in partial fulfilment of the requirements for the degree of Master of Science. Department of Biochemistry, Mc Gill University, Montreal. September 1961 i ABSTRACT The writer has developed an as say for estimation of optimal hexokinase activity in stroma-free hemolyzate, and shawn that hexokinase remains stable and active for at least 30 days in human erythrocytes preserved in CD or ACD at 4 ° C. Addition of ADP or DPN to the assay medium could increase the enzyme 1s activity; nicotinamide or alloxan depressed it. It is suggested that failure of glycolytic activity during preservation is not therefore due to the formerly supposed lability of hexokinase, but to inhibition of hexokinase attributable to falling pH and ATP, and conditions favouring glucose-6-P accumulation such as decrease of phosphofructokinase, DPN and ADP. Pyruvate produced in cells during the first 15 days of storage tended to be expelled into the external medium. Cyclic adenylate was utilised by the human red cell, as evidenced by conversion of its ribose moiety into lactic acid with concomitant esterification of inorganic phosphate into the stable phosphate fraction. ii AC KNOWLEDGE MEN TS I am most grateful to Dr. O. F. Denstedt for his sympathetic guidance and understanding throughout the course of this investigation. The kindness and spirit of my colleagues are greatly appreciated and I wish to express my thanks to Mrs. Marina van Ermengen, Miss Anne Hemphill and Miss Arlene Maximchuk for assistance in some of the experimenta, and to Miss Maximchuk for proofreading the manuscript.
    [Show full text]
  • Bio-Based Route to the Carbon-5 Chemical Glutaric Acid and Bio-Polyamide PA6.5 Using Metabolically Engineered Corynebacterium Glutamicum
    Electronic Supplementary Material (ESI) for Green Chemistry. This journal is © The Royal Society of Chemistry 2018 Online Supplementary Information to: Bio-based route to the carbon-5 chemical glutaric acid and bio-polyamide PA6.5 using metabolically engineered Corynebacterium glutamicum Submitted for publication to Green Chemistry Christina Maria Rohlesa, Lars Gläsera, Michael Kohlstedta, Gideon Gießelmanna, Samuel Pearsonb, Aránzazu del Campob, Judith Beckera, and Christoph Wittmanna* a. Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany b. Leibniz Institut für Neue Materialien, Saarbrücken, Germany * Phone: +49-(0) 681 302 71970, E-mail: [email protected] Annotations and abbreviations of genes in central carbon metabolism and lysine biosynthesis (addendum to Figure 1). aceA: isocitrate lyase; aceB: malic synthase; aceEF: subunits of pyruvate dehydrogenase; acn: aconitase; ald: aldolase; asd: aspartate semialdehyde dehydrogenase; aspB: aspartate aminotransferase; dapA: dihydrodipicolinate synthase; dapB: dihydrodipicolinate reductase; dapC: succinyl-amino-ketopimelate transaminase; dapD: tetrahydrodipicolinate succinylase; dapE: succinyl- diaminopimelate desuccinylase; dapF: diaminopimelate epimerase; ddh: diaminopimelate dehydrogenase; eno: enolase; fbp: fructose 1,6-bisphosphatase; fum: fumarase; gapA: glyceraldehyde 3-phosphate dehydrogenase; gltA: citrate synthase; homV59A: homoserine dehydrogenase with amino acid exchange valine to alanine at position 59; icdA1G: isocitrate dehydrogenase
    [Show full text]
  • The Biological Role of the RBP7910 Z-Binding Protein in the Mitochondrial Mrna Processing of Trypanosoma Brucei
    The biological role of the RBP7910 Z-binding protein in the mitochondrial mRNA processing of Trypanosoma brucei Nisha Ramamurthy Department of Parasitology McGill University Montréal, Canada August 2020 A thesis submitted to McGill University in partial fulfillment of the requirements of the degree of Master of Science ©Nisha Ramamurthy, 2020 1 Table of contents 1. List of Figures and Tables .................................................................................................... 4 2. List of Abbreviations ............................................................................................................ 6 3. Abstract .................................................................................................................................. 7 4. Acknowledgments ................................................................................................................. 9 5. Introduction and Literature review .................................................................................. 10 5.1 Kinetoplastids: Occurrence, Prevalence and Importance ............................................... 10 5.2 Life cycle of T.brucei: .................................................................................................... 11 5.3 Energy regulation in T. brucei: ...................................................................................... 12 5.4 Differentiation between procyclic forms (PFs) and bloodstream forms (BFs): ............. 14 5.5 RNA editing regulated in a life-stage specific manner .................................................
    [Show full text]
  • Glycogen Metabolism Glycogen Breakdown Glycogen Synthesis
    Glycogen Metabolism Glycogen Breakdown Glycogen Synthesis Control of Glycogen Metabolism Glycogen Storage Diseases Glycogen Glycogen - animal storage glucan 100- to 400-Å-diameter cytosolic granules up to 120,000 glucose units α(1 → 6) branches every 8 to 12 residues muscle has 1-2% (max) by weight liver has 10% (max) by weight ~12 hour supply Although metabolism of fat provides more energy: 1. Muscle mobilize glycogen faster than fat 2. Fatty acids of fat cannot be metabolized anaerobically 3. Animals cannot convert fatty acid to glucose (glycerol can be converted to glucose) Glycogen Breakdown Three enzymes: glycogen phosphorylase glycogen debranching enzyme phosphoglucomutase Glycogen phosphorylase (phosphorylase) - phosphorolysis of glucose residues at least 5 units from branch point Glycogen + Pi glycogen + glucose-1-phosphate (n residues) (n-1 residues) homodimer of 842-residues (92-kD) subunits allosteric regulation - inhibitors (ATP, glucose-6- phosphate, glucose) and activator (AMP), T ⇔ R covalent modification (phosphorylation) - modification/demodification 2- phosphorylase a (active, SerOPO3 ) phosphorylase b (less active, Ser) narrow 30-Å crevice binds glycogen, accommodates 4 to 5 residues Pyridoxal-5-phosphate (vit B6 derivative) cofactor - located near active site, general acid-base catalyst Rapid equilibrium Random Bi Bi kinetics Glycogen Breakdown Glycogen debranching enzyme - possesses two activities α(1 → 4) transglycosylase (glycosyl transferase) 90% glycogen → glucose-1-phosphate transfers trisaccharide unit from
    [Show full text]
  • Changes in Brain Gene Expression Shared by Scrapie and Alzheimer
    Proc. Nati. Acad. Sci. USA Vol. 86, pp. 7260-7264, September 1989 Neurobiology Changes in brain gene expression shared by scrapie and Alzheimer disease (Pick disease/sulfated glycoprotein 2/transferrin/glial fibrillary acidic protein/metaflothionein) JOHN R. DUGUID*tt, CRAIG W. BOHMONT*, NINGAI LIU*t, AND WALLACE W. TOURTELLOTTE§¶ *Geriatric Research, Education and Clinical Center, Edith N. Rogers Memorial Veterans Hospital, Bedford, MA, 01730; Departments of tBiochemistry and SNeurology, Boston University School of Medicine, Boston, MA 02118; Neurology Service, Wadsworth Veterans Administration Medical Center, Los Angeles, CA 90073; and IDepartment of Neurology, University of California, Los Angeles, CA 90024 Communicated by Walle J. H. Nauta, June 19, 1989 (receivedfor review January 5, 1989) ABSTRACT We have isolated two recombinant cDNAs study the single-stranded scrapie library DNA (25 Lg ) was whose corresponding RNAs have an increased abundance in hybridized successively with 50, 25, and 25 ,ug of sonicated, scrapie-infected hamster brain. DNA sequence analysis has biotinylated control library DNA (2.5 ,ug/Al) for 20 hr at 680C shown that these two recombinants represent the genes for in 0.75 M NaCl/25 mM Hepes/5 mM EDTA/0.1% sodium sulfated glycoprotein 2 and transferrin. The abundance of dodecyl sulfate, pH 7.5, containing poly(A) and poly(C) sulfated glycoprotein 2 RNA is increased in hippocampus from (Pharmacia) at 10 ,ug/ml. After each cycle the DNA was patients with Alzheimer disease and Pick disease, whereas subjected to the stringency incubation, subtracted with avi- transferrin RNA is not strongly modulated in these conditions. din-biocytin-Sephacryl 1000 resin (4 ,ul ofpacked resin per ,ug Expression of two previously identified scrapie-modulated of biotinylated DNA), and denatured as described (8).
    [Show full text]
  • 12) United States Patent (10
    US007635572B2 (12) UnitedO States Patent (10) Patent No.: US 7,635,572 B2 Zhou et al. (45) Date of Patent: Dec. 22, 2009 (54) METHODS FOR CONDUCTING ASSAYS FOR 5,506,121 A 4/1996 Skerra et al. ENZYME ACTIVITY ON PROTEIN 5,510,270 A 4/1996 Fodor et al. MICROARRAYS 5,512,492 A 4/1996 Herron et al. 5,516,635 A 5/1996 Ekins et al. (75) Inventors: Fang X. Zhou, New Haven, CT (US); 5,532,128 A 7/1996 Eggers Barry Schweitzer, Cheshire, CT (US) 5,538,897 A 7/1996 Yates, III et al. s s 5,541,070 A 7/1996 Kauvar (73) Assignee: Life Technologies Corporation, .. S.E. al Carlsbad, CA (US) 5,585,069 A 12/1996 Zanzucchi et al. 5,585,639 A 12/1996 Dorsel et al. (*) Notice: Subject to any disclaimer, the term of this 5,593,838 A 1/1997 Zanzucchi et al. patent is extended or adjusted under 35 5,605,662 A 2f1997 Heller et al. U.S.C. 154(b) by 0 days. 5,620,850 A 4/1997 Bamdad et al. 5,624,711 A 4/1997 Sundberg et al. (21) Appl. No.: 10/865,431 5,627,369 A 5/1997 Vestal et al. 5,629,213 A 5/1997 Kornguth et al. (22) Filed: Jun. 9, 2004 (Continued) (65) Prior Publication Data FOREIGN PATENT DOCUMENTS US 2005/O118665 A1 Jun. 2, 2005 EP 596421 10, 1993 EP 0619321 12/1994 (51) Int. Cl. EP O664452 7, 1995 CI2O 1/50 (2006.01) EP O818467 1, 1998 (52) U.S.
    [Show full text]
  • GC/MS-Based Differential Metabolic Profiling of Human Peptic Ulcer Disease to Study Helicobacter Pylori-Induced Metabolic Pertur
    BIOCELL Tech Science Press 2021 GC/MS-based differential metabolic profiling of human peptic ulcer disease to study Helicobacter pylori-induced metabolic perturbations GAGANJOT GUPTA1;DEEPAK BANSAL2;ANSHULA SHARMA1;TAWSEEF AHMAD1;ATUL SACHDEV2;AJAZ AHMAD3; HAMED A. EL-SEREHY4;BALJINDER KAUR1,* 1 Department of Biotechnology, Punjabi University, Patiala, 147002, India 2 Department of Gastroenterology, Government Medical College and Hospital, Chandigarh, 160047, India 3 Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia 4 Department of Zoology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia Key words: Peptic ulcer disease, Gastric cancer, Helicobacter pylori, Metabolic profiling, Perturbations, Stomach ulcers Abstract: Helicobacter pylori infection has been significantly linked to Peptic Ulcer Disease and Gastric Cancer. Metabolomic fingerprinting may offer a principal way of early diagnosis and to understand the molecular mechanism of H. pylori-induced pathogenicity. The rationale of the study is to explore the underlying distinct metabolic mechanisms of H. pylori-induced PUD and to identify potential biomarkers for disease diagnosis and associated risks using Gas chromatography/mass spectrometry. GC/MS-based analytical method was used to compare metabolic profiles of healthy controls (N = 20) and peptic ulcer patients (N = 45). Acquired metabolomic data were analyzed by constructing a diagnostic model using principal component analysis and a non-parametric two-tailed paired Wilcoxon analysis to identify disease-specific metabolic biomarkers. A total of 75 low-molecular-weight endogenous metabolites were detected during comparative metabolomic analysis of PUD vs. healthy gut tissues, among which 16 metabolites are being proposed to be diagnostic markers of Human PUD.
    [Show full text]
  • Modeling and Simulation of the Redox Regulation of the Metabolism in Escherichia Coli at Diferent Oxygen Concentrations Yu Matsuoka1 and Hiroyuki Kurata1,2*
    Matsuoka and Kurata Biotechnol Biofuels (2017) 10:183 DOI 10.1186/s13068-017-0867-0 Biotechnology for Biofuels RESEARCH Open Access Modeling and simulation of the redox regulation of the metabolism in Escherichia coli at diferent oxygen concentrations Yu Matsuoka1 and Hiroyuki Kurata1,2* Abstract Background: Microbial production of biofuels and biochemicals from renewable feedstocks has received consider- able recent attention from environmental protection and energy production perspectives. Many biofuels and bio- chemicals are produced by fermentation under oxygen-limited conditions following initiation of aerobic cultivation to enhance the cell growth rate. Thus, it is of signifcant interest to investigate the efect of dissolved oxygen concen- tration on redox regulation in Escherichia coli, a particularly popular cellular factory due to its high growth rate and well-characterized physiology. For this, the systems biology approach such as modeling is powerful for the analysis of the metabolism and for the design of microbial cellular factories. Results: Here, we developed a kinetic model that describes the dynamics of fermentation by taking into account transcription factors such as ArcA/B and Fnr, respiratory chain reactions and fermentative pathways, and catabolite regulation. The hallmark of the kinetic model is its ability to predict the dynamics of metabolism at diferent dissolved oxygen levels and facilitate the rational design of cultivation methods. The kinetic model was verifed based on the experimental data for a wild-type E. coli strain. The model reasonably predicted the metabolic characteristics and molecular mechanisms of fnr and arcA gene-knockout mutants. Moreover, an aerobic–microaerobic dual-phase culti- vation method for lactate production in a pf-knockout mutant exhibited promising yield and productivity.
    [Show full text]
  • Protrudin and PDZD8 Contribute to Neuronal Integrity by Promoting Lipid
    ARTICLE https://doi.org/10.1038/s41467-020-18413-9 OPEN Protrudin and PDZD8 contribute to neuronal integrity by promoting lipid extraction required for endosome maturation ✉ Michiko Shirane1 , Mariko Wada1, Keiko Morita1, Nahoki Hayashi1, Reina Kunimatsu1, Yuki Matsumoto1, ✉ Fumiko Matsuzaki2, Hirokazu Nakatsumi1, Keisuke Ohta 3, Yasushi Tamura4 & Keiichi I. Nakayama 2 1234567890():,; Endosome maturation depends on membrane contact sites (MCSs) formed between endo- plasmic reticulum (ER) and endolysosomes (LyLEs). The mechanism underlying lipid supply for this process and its pathophysiological relevance remains unclear, however. Here, we identify PDZD8—the mammalian ortholog of a yeast ERMES subunit—as a protein that interacts with protrudin, which is located at ER-LyLE MCSs. Protrudin and PDZD8 promote the formation of ER-LyLE MCSs, and PDZD8 shows the ability to extract various lipids from the ER. Overexpression of both protrudin and PDZD8 in HeLa cells, as well as their depletion in mouse primary neurons, impairs endosomal homeostasis by inducing the formation of abnormal large vacuoles reminiscent of those apparent in spastin- or REEP1-deficient neu- rons. The protrudin-PDZD8 system is also essential for the establishment of neuronal polarity. Our results suggest that protrudin and PDZD8 cooperatively promote endosome maturation by mediating ER-LyLE tethering and lipid extraction at MCSs, thereby maintaining neuronal polarity and integrity. 1 Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan. 2 Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, Japan. 3 Department of Anatomy, Kurume University School of Medicine, Kurume, Fukuoka, Japan. 4 Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata, Yamagata, ✉ Japan.
    [Show full text]
  • Barr Virus Latent Membrane Protein 1- Mediated NF-Κb Activation
    Investigation of the mechanism of Epstein- Barr Virus Latent Membrane Protein 1- mediated NF-κB activation. Dissertation zur Erlangung des akademischen Grades des Doktors der Naturwissenschaften (Dr. rer. nat.) eingereicht im Fachbereich Biologie, Chemie, Pharmazie der Freien Universität Berlin vorgelegt von Daniela Böhm aus Mittweida Februar 2010 Die Arbeit wurde von März 2006 bis September 2009 im Labor von Prof. Elliott Kieff und Prof. Ellen Cahir- McFarland im Department of Microbiology and Molecular Genetics, Harvard Medical School and Department of Medicine, Division of Infectious Disease, Brigham and Woman’s Hospital in Boston, MA, USA unter der Leitung von Prof. Ellen Cahir-McFarland angefertigt. 1. Gutachter: Prof. Ellen Cahir-McFarland 2. Gutachter: Prof. Volker Haucke Disputation am: 27.April 2010 2 Acknowledgments ACKNOWLEDGMENTS I would like to thank Prof. Ellen D. Cahir McFarland and Prof. Elliott Kieff for giving me the opportunity to complete my thesis in their laboratory. Furthermore, I sincerely thank Ellen D. Cahir McFarland for her great guidance and support throughout my work. In addition, I thank all the members of the Kieff/ Muenger/ Kaye and Wang laboratories at the 8 th floor of the Channing lab, especially Mike Calderwood, Ben Gewurz, Aline Habison, Chantal Beauchemin, Kevin Hall, Amy Holthaus, Olga Saturne, Vishal Soni, Thomas Sommermann, Nick Shinners, and Jae Song. 5 Table of contents 1. INTRODUCTION ................................................................................................................
    [Show full text]